PubMed Health⌕ Search

Biomedical subjects

J Lalucat

Publications and source records attributed to J Lalucat.

At least 19 recordsLinked to original sources
PubMed2006

A molecular microbial ecology approach to studying hemodialysis water and fluid.

Bacteria, or bacteria-derived products, might be responsible for deleterious effects in hemodialysis patients. Most microorganisms in hemodialysis water, including potential pathogens, are difficult to isolate and might subsist in a 'viable but not culturable' state or may need specific culture media. A molecular culture-independent approach based on the analysis of the 16S rDNA obtained from total DNA has been used to better know the diversity of bacteria inhabiting hemodialysis water and fluid, and to address the possible health effects associated with their presence. Four clone libraries from 16S rDNA (274 clones) were analyzed to characterize the species or groups of bacteria present, to assess their distribution in the water circuit, and to compare the results with those previously obtained in culture-dependent analysis. One hundred and ninety-seven clones of four gene libraries were analyzed by sequencing, and were identified phylogenetically. Clones affiliated to the Alphaproteobacteria group led the diversity. The presence in several samples of Alpha-4-proteobacteria, recognized as sphingolipids producers, was to be noted. The most abundant clones were affiliated to the Betaproteobacteria branch, closely related to the genus Herbaspirillum. As known, Alphaproteobacteria and Betaproteobacteria genomes might present a manifest excess in CpG sequences and most of them show a lipopolysaccharide-rich outer membrane, both described as inducers of innate immunity responses. Another abundant group, belonging to the Cyanobacteria class, a possible source of cyanotoxins, was not related to any previously cultured bacterium. Possible risk implications for hemodialysis patients of the bacterial community detected are discussed.

Alphaproteobacteria↗
PubMed2001

Pseudomonas sp. strain KC represents a new genomovar within Pseudomonas stutzeri.

Pseudomonas sp. strain KC (= ATCC 55595 = DSM 7136) is a denitrifying aquifer isolate that produces and secretes pyridine-2,6-bis(thiocarboxylate) (PDTC), a chelating agent that fortuitously transforms carbon tetrachloride without producing chloroform. Although KC has been used successfully for full-scale bioremediation of carbon tetrachloride, its taxonomy has proven difficult to resolve, as it retains properties of both Pseudomonas stutzeri and Pseudomonas putida. In the present work, a polyphasic approach was used to conclude that strain KC represents a new genomovar (genomovar 9) within the species P. stutzeri.

Biodegradation, Environmental↗
PubMed2001

Clonal population structure of Pseudomonas stutzeri, a species with exceptional genetic diversity.

Genetic diversity and genetic relationships among 42 Pseudomonas stutzeri strains belonging to several genomovars and isolated from different sources were investigated in an examination of 20 metabolic enzymes by multilocus enzyme electrophoresis analysis. Forty-two distinct allele profiles were identified, indicating that all multilocus genotypes were represented by a single strain. All 20 loci were exceptionally polymorphic, with an average of 15.9 alleles per locus. To the best of our knowledge, this P. stutzeri sample exhibited the highest mean genetic diversity (H = 0.876) found to date in all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles was identified. The index of association (I(A)) for the P. stutzeri strains analyzed was 1.10. The I(A) values were always significantly different from zero for all subgroups studied, including clinical and environmental isolates and strains classified as genomovar 1. These results suggest that the population structure of P. stutzeri is strongly clonal, indicating that there is no significant level of assortative recombination that might destroy linkage disequilibrium.

Alleles↗
PubMed2000

Utility of internally transcribed 16S-23S rDNA spacer regions for the definition of Pseudomonas stutzeri genomovars and other Pseudomonas species.

Bacteria identified and classified as Pseudomonas stutzeri, on the basis of traditional criteria, are recognized to be markedly heterogeneous, such that a systematic phenotypic characterization has not been correlated with genotypic groupings (i.e. genomovars) based upon DNA-DNA similarities. The internally transcribed 16S-23S rDNA spacer (ITS1) regions of P. stutzeri were analysed with respect to the ability of these nucleic acid regions to differentiate and identify the genomic groups (i.e. genomovars) of P. stutzeri. The ITS1s of 34 strains of P. stutzeri were amplified by PCR and the PCR product was subjected to RFLP analysis, which allowed the differentiation and identification of the strains to their respective genomovars. Sequence determination and analysis of ITS1s supported further the results obtained by RFLP, i.e. nucleotide signatures were identified in strains belonging to different genomovars. The ITS1s of all strains of P. stutzeri contained the tandem tRNA(Ile)/tRNA(Ala) genes and did not exhibit distinct sequence heterogeneity between different operons of a strain. Phylogenetically informative variable sites were located, exclusively, in non-coding regions. The results of the RFLP and sequence analysis of ITS1s supported and correlated with the phylogenetic relationships estimated from 16S rRNA gene sequence comparisons and DNA-DNA hybridizations, offering an alternative tool for genomovar and species differentiation.

DNA, Bacterial↗
PubMed2000

Rapid identification of Salmonella typhimurium, S. enteritidis and S. virchow isolates by polymerase chain reaction based fingerprinting methods.

In this study we used and evaluated three rapid molecular typing methods for the identification of three frequent, clinically significant Salmonella serovars on the basis of the ease, simplicity and reproducibility of the chosen methods. We determined the genetic diversity among several isolates of Salmonella enteritidis, S. typhimiurium and S. virchow, and compared them with other enterobacteria by using the repetitive extragenic palindromic (REP) sequences, the enterobacterial repetitive intergenic consensus (ERIC) sequences, and the 16S-23S rDNA intergenic spacer region (ITS 1). The objective was to evaluate their potential application to discriminate among members of the species Salmonella enterica subspecies enterica using the genetic diversity of the group found by genomic fingerprinting. The three different serovars of Salmonella studied gave reproducible and distinguishable profiles using whichever of the above mentioned polymerase chain reaction (PCR) methods assayed. The conserved patterns in each serovar allowed for easy differentiation from other serovars of Salmonella.

Bacterial Typing Techniques↗
PubMed1998

Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov.

The taxonomic relationship between several Shewanella putrefaciens isolates from the Baltic Sea and reference strains of this species is presented in this study. Results from DNA-DNA hybridization using a newly developed non-radioactive detection system and from 16S rRNA gene sequencing demonstrated that S. putrefaciens is a heterogeneous species containing more than a single genomic group. The genomic group II was phylogenetically, genotypically and phenotypically distant enough from the species type strain to be classified as a single species within the genus Shewanella. Therefore, we propose to reclassify Owen's genomic group II as Shewanella baltica sp. nov. with the type strain NCTC 10735.

DNA, Bacterial↗
PubMed1998

Genetic relationships among Pseudomonas stutzeri strains based on molecular typing methods.

Detailed characterization of the genetic variability among strains belonging to Pseudomonas stutzeri was achieved using different rapid molecular typing methods based on polymerase chain reaction (PCR), Southern blot and Western blot. Consensus motifs complementary to fragments of repetitive elements dispersed throughout the genomes of bacteria were used as primers and allowed differentiation at subspecies levels. Further and simple differentiation was also achieved based on the direct amplification of spacer regions between 16S and 23S rRNA, combined with single-strand conformation polymorphism (SSCP) analysis of the generated fragments. These methods are fast, sensitive, reliable for determining relationships, and have demonstrated a great genetic diversity among the strains of Ps. stutzeri studied in agreement with the heterogeneous phenotypic traits of the species.

Bacterial Typing Techniques↗
PubMed1997

Genome organization of Pseudomonas stutzeri and resulting taxonomic and evolutionary considerations.

In order to determine the genome variability within Pseudomonas stutzeri, 20 strains representing the seven described genomovars and strain JM300 were analyzed by using various resolution levels of rare cutting enzymes. XbaI and SpeI fingerprints revealed a high degree of heterogeneity of restriction patterns that did not correlate with the division into genomovars. However, a fragment pattern comparison led to the establishment of several groups of clonal variants within genomovars. One circular chromosome ranging in size from 3.75 to 4.64 Mb constitutes the genome of P. stutzeri strains. The I-CeuI, PacI, and SwaI low-resolution map of P. stutzeri type strain CCUG 11256 shows the locations of 12 genes, including rrn operons and the origin of replication. I-CeuI digests of the 20 strains studied plus the positions of six genes allowed a comparison of the rrn backbone organization within genomovars; the four rrn operons seemed to be at similar locations with respect to the origin of replication, as did the rest of the genes. However, a comparison of I-CeuI cleavage maps of the genomovar reference strains revealed a diverse genome organization in the genomovars relative to rrn operons and gene locations. In most genomovars, rrn operons are not arranged around the origin of replication but are equally distributed on the chromosome. Strain JM300 does not belong to any described genomovar, as determined from the organization of its genome. Large chromosomal rearrangements seem to be responsible for the differences in superordinate genome structure and must have played an important role in P. stutzeri diversification and niche colonization. An ancestral chromosome is suggested, and some plausible pathways for the generation of the various genome structures are proposed.

Blotting, Southern↗
PubMed1997

Vibrio scophthalmi sp. nov., a new species from turbot (Scophthalmus maximus).

Six strains isolated from the intestines of juvenile turbot in a fish hatchery in the north of Spain were found to be phenotypically members of the genus Vibrio. However, the phenotypic traits of these organisms did not place them in any of the currently known Vibrio species. These isolates formed an homogeneous group in which the DNA-DNA similarity values (the differences between the thermal denaturation midpoints of the homologous and heterologous duplexes) with reference strain A089T (T = type strain) ranged from 0 to 1.7 degrees C. The results of a 16S rRNA sequence analysis of A089T placed this strain in the genus Vibrio in the gamma subclass of the Proteobacteria. The closest relative is Vibrio aestuarianus, with a sequence similarity of 97.8%. This group of strains can be easily differentiated from the other Vibrio species by their clear phenotype. We propose the name Vibrio scophthalmi sp. nov. for these strains; the type strain is strain A089 (= CECT 4638).

Animals↗
PubMed1997

Pseudoalteromonas antarctica sp. nov., isolated from an Antarctic coastal environment.

The taxonomic characteristics of five bacterial strains which were isolated from Antarctic coastal marine environments were studied. These bacteria were psychrotrophic, aerobic, and gram negative with polar flagella. The G + C contents of the DNAs of these strains were 41 to 42 mol%. The Antarctic strains were phenotypically distinct from the previously described Pseudoalteromonas type species. DNA-DNA hybridization experiments revealed that the new strains were closely related to each other but clearly different from Pseudoalteromonas haloplanktis and Pseudoalteromonas atlantica, which were the most phenotypically similar organisms. None of the bacterial isolates was capable of using DL-malate, D-sorbitol, or m-hydroxybenzoate, and all were capable of gelatin hydrolysis. Strains NF2, NF3T (T = type strain), NF13, NF14, and EN10 had an Na+ requirement but required only 17 mM Na+. Phenotypic, DNA G + C content, DNA-DNA hybridization, 16S rRNA analysis, fatty acid composition, and protein profile data confirmed the identification of the Antarctic strains as members of a Pseudoalteromonas sp. The name Pseudoalteromonas antarctica sp. nov. is proposed for these organisms.

Antarctic Regions↗
PubMed1996

16S rRNA gene sequence analysis relative to genomovars of Pseudomonas stutzeri and proposal of Pseudomonas balearica sp. nov.

We compared the 16S rRNA gene sequences of 14 strains of Pseudomonas stutzeri, including type strain CCUG 11256 and strain ZoBell (= ATCC 14405), which represented the seven P. stutzeri genomovars (DNA-DNA similarity groups) that have been described. Our sequence analysis revealed clusters which were highly correlated with genomovar clusters derived from DNA-DNA hybridization data. In addition, we identified signature nucleotide positions for each genomovar. We found that the 16S rRNA gene sequences of genomovar 6 strains SP1402T (T = type strain) and LS401 were different enough from the sequence of the type strain of P. stutzeri that these organisms should be placed in a new species, Pseudomonas balearica. The type strain of P. balearica is strain SP1402 (= DSM 6083).

Base Sequence↗
PubMed1994

Comparative biochemical and genetic analysis of naphthalene degradation among Pseudomonas stutzeri strains.

Of a 49-strain collection of Pseudomonas stutzeri species, 11 isolates were able to degrade naphthalene and 1 isolate was able to use m- and p-toluate as sole carbon and energy sources. Of these 12 strains, 10 shared a highly homologous set of naphthalene catabolic genes, even though they belong to four different genomovars. These genes differed from those present in plasmid NAH7. In only one of these degraders could a plasmid-encoded pathway be demonstrated, and a chromosome-encoded pathway is proposed for the remaining strains. meta cleavage of catechol was only observed in those strains able to metabolize alkyl derivatives of catechol.

Biodegradation, Environmental↗
PubMed1991

Velocity changes, long runs, and reversals in the Chromatium minus swimming response.

The velocity, run time, path curvature, and reorientation angle of Chromatium minus were measured as a function of light intensity, temperature, viscosity, osmotic pressure, and hydrogen sulfide concentration. C. minus changed both velocity and run time. Velocity decreased with increasing light intensity in sulfide-depleted cultures and increased in sulfide-replete cultures. The addition of sulfide to cultures grown at low light intensity (10 microeinsteins m-2 s-1) caused mean run times to increase from 10.5 to 20.6 s. The addition of sulfide to cultures grown at high light intensity (100 microeinsteins m-2 s-1) caused mean run times to decrease from 15.3 to 7.7 s. These changes were maintained for up to an hour and indicate that at least some members of the family Chromatiaceae simultaneously modulate velocity and turning frequency for extended periods as part of normal taxis.

Cell Movement↗
PubMed1989

R-body-producing bacteria.

Until 10 years ago, R bodies were known only as diagnostic features by which endosymbionts of paramecia were identified as kappa particles. They were thought to be limited to the cytoplasm of two species in the Paramecium aurelia species complex. Now, R bodies have been found in free-living bacteria and other Paramecium species. The organisms now known to form R bodies include the cytoplasmic kappa endosymbionts of P. biaurelia and P. tetraurelia, the macronuclear kappa endosymbionts of P. caudatum, Pseudomonas avenae (a free-living plant pathogen), Pseudomonas taeniospiralis (a hydrogen-oxidizing soil microorganism), Rhodospirillum centenum (a photosynthetic bacterium), and a soil bacterium, EPS-5028, which is probably a pseudomonad. R bodies themselves fall into five distinct groups, distinguished by size, the morphology of the R-body ribbons, and the unrolling behavior of wound R bodies. In recent years, the inherent difficulties in studying the organization and assembly of R bodies by the obligate endosymbiont kappa, have been alleviated by cloning and expressing genetic determinants for these R bodies (type 51) in Escherichia coli. Type 51 R-body synthesis requires three low-molecular-mass polypeptides. One of these is modified posttranslationally, giving rise to 12 polypeptide species, which are the major structural subunits of the R body. R bodies are encoded in kappa species by extrachromosomal elements. Type 51 R bodies, produced in Caedibacter taeniospiralis, are encoded by a plasmid, whereas bacteriophage genomes probably control R-body synthesis in other kappa species. However, there is no evidence that either bacteriophages or plasmids are present in P. avenae or P. taeniospiralis. No sequence homology was detected between type 51 R-body-encoding DNA and DNA from any R-body-producing species, except C. varicaedens 1038. The evolutionary relatedness of different types of R bodies remains unknown.

Animals↗
PubMed1988

New naphthalene-degrading marine Pseudomonas strains.

Over 100 strains that utilized naphthalene as the only carbon and energy source were isolated from samples of marine sediments taken from a heavily polluted area. The isolates were characterized taxonomically and physiologically. Most of these strains belonged to the genus Pseudomonas, and seven of them did not fit any previous taxonomic description. They differed from type strains in a few biochemical characteristics and in the utilization of aromatic compounds. None had catechol 1,2-dioxygenase activity, and catechol 2,3-dioxygenase was responsible for the aromatic ring cleavage. DNA hybridization demonstrated a close relationship between two isolates and the Pseudomonas stutzeri type strain, and between five isolates and the Pseudomonas testosteroni type strain. On the basis of nutritional and enzymatic characteristics, it was assumed that the seven isolates represent new biovars belonging to the species P. testosteroni and P. stutzeri that are able to degrade aromatic hydrocarbons.

Biodegradation, Environmental↗
PubMed1986

Comparative study of refractile (R) bodies and their genetic determinants: relationship of type 51 R bodies to R bodies produced by Pseudomonas taeniospiralis.

The relationship of type 51 refractile (R) bodies to R bodies produced by Pseudomonas taeniospiralis was investigated. Proteins associated with type 51 R bodies were not serologically cross-reactive with proteins associated with R bodies from P. taeniospiralis. The genetic determinants for type 51 R bodies did not exhibit close homology with DNA sequences from P. taeniospiralis.

Bacteria↗